Hi Matt, Thank you for letting me know. The full command I mentioned is as follows:
probtrackx2 --samples=../T1w/Diffusion.bedpostX/merged \ --mask=../T1w/Diffusion.bedpostX/nodif_brain_mask \ --xfm=xfms/standard2acpc_dc \ --invxfm=xfms/acpc_dc2standard --seedref=T1w_restore.2.nii.gz \ --loopcheck --forcedir -c 0.2 --sampvox=2 --randfib=1 \ --stop=Connectome/stop --wtstop=Connectome/wtstop \ --waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \ -x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \ --target3=Connectomes/GrayOrdinates.txt --dir=Connectomes It's in the HCP course practical "Fibre Orientation Models and Tractography Analysis" taught by Matteo Bastiani. Thank you. ________________________________ From: Glasser, Matthew <glass...@wustl.edu> Sent: Thursday, April 25, 2019 7:04 PM To: Aaron C; hcp-users@humanconnectome.org Cc: Stamatios Sotiropoulos Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome Not as far as I am aware, but Stam might know. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> Date: Thursday, April 25, 2019 at 9:15 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Probabilistic tractography for dense connectome Dear HCP experts, I have a question about the probabilistic tractography command used for generating dense connectome (https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7). Are there any shared scripts for generating "pial.L.asc", "white.L.asc", "Whole_Brain_Trajectory_ROI_2.nii.gz", and the files such as "CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz" used in the probabilistic tractography command? _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
